The genetic structure of a human population can be described in terms of two principal parameters: the inbreeding coefficient and gene frequency array. The inbreeding coefficient specifies the correlation between uniting gametes, and therefore alleles, in a given gene pool. Allele or gene frequency is a fundamental quantity by which to describe the wide occurrence of genetic polymorphisms in man. Recent advances in molecular biology have confirmed the existence of multiple alleles at a single locus, as well as multiple loci which are linked on the same chromosome.

This paper attempts to unify formulae for estimating allele frequency from population samples, by a counting method. It also presents quantities expressed in terms of allele frequencies, polymorphic information content (PIC) and probability of paternity exclusion (PE). These are of interest in genetic epidemiology.

With desktop computers there is little difficulty in using mathematically quite sophisticated methods such as maximum likelihood, but handy formulae are still indispensable and sound algorithms are required. Many genetic systems can now be treated as codominant, but some are still complicated by dominance. In the following, calculation procedures are given using codominant systems and the ABO-like systems.

Allele frequency estimations

The codominant system

Consider a locus A, with two alleles A1 and A2. Let the frequency of Ai be pi (i = 1 and 2). The expected frequency of the three genotypes, A1A1, A2A2 and A1A2, in a random mating population, will be p12, P22 and 2p1P2, respectively.